With performance against Bills, Smith now leads the NFL in passer rating as Giants come to San Francisco in rematch of NFC Championship Game

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Niners QB Alex Smith (right) has led San Francisco to a 4-1 record this season. (Photo by Joe Robbins/Getty Images)

Updated at 12:48 PM PDT on Tuesday, Oct 9, 2012

After leading his team to the NFC West title and the NFC Championship Game last season, La Mesa's Alex Smith was a man without a job.

Though as a free agent he was told the 49ers wanted to re-sign him, Smith waited and waited and waited … and watched as the Niners showed some interest in Peyton Manning after Manning was set free by the Colts.

In the end, however, Smith signed a three-year deal with the 49ers. Yet the Niners’ flirtation with Manning caused some outside the organization to wonder if Smith’s confidence had been damaged at all by the fact his team had pondered going in another direction.

Five games into this 2012 season, those questions now seem silly.

Smith not only has led the 49ers to a 4-1 start, he’s playing even better than he did last season when he posted the best statistics of his career.

This year, Smith leads the NFL in passer rating (108.7) – ahead of Matt Ryan, Tom Brady and Manning – and has thrown for 1,087 yards while completing 68.6 percent of his passes for eight TDs against just one interception.

On Sunday, Smith had perhaps the best game of his seven-year NFL career, throwing for 303 yards and three scores in a 45-3 rout of the Buffalo Bills. His passing performance included a flurry of downfield throws, with six completions of more than 19 yards.

Said head coach Jim Harbaugh of Smith, who connected on 18-of-24 passes: “Quarterback was near perfect.”

Smith’s new status as the league’s highest-ranking quarterback is a drastic turnaround from two seasons ago, when he lost his starting job and was a favorite target of disgruntled 49ers fans. As Eric Branch of the San Francisco Chronicle noted this week: “Smith’s ascension to the top comes two years after his career hit rock bottom: On Oct. 10, 2010, Smith was booed mercilessly by the Candlestick Parks fans in a 27-24 loss to the Eagles, better known as the ‘We-want-Carr!’ game” (a chant for backup QB David Carr).

Last season, while often termed a “game manager,” Smith set a career high for quarterback rating (90.7) and led several late-game comebacks, including a memorable performance against the Saints in the playoffs when he ran for a fourth-quarter score and connected with tight end Vernon Davis on the game-winner.

This season, he’s not being called a game manager any more. With some new receivers and more confidence and knowledge of the Niners offense, Smith is playing like one of the NFL’s best quarterbacks.

His QB rating against the Bills (156.2) was almost perfect and was the highest by any NFL quarterback in 23 weeks of the regular season.

As Smith and the 49ers prepare to play the New York Giants this Sunday at Candlestick Park in a rematch of last season’s NFC Championship Game, Harbaugh says Smith has continued to grow.

“I can’t tell you how much respect I have for him,” Harbaugh told reporters this week, adding that Smith is a much better NFL quarterback than he was. “He plays so well, handles himself. He does all the things. I look back and say, ‘I wish I could have done as good a job as he’s done on and off the field.”

Though Harbaugh said he’s concerned about Smith's sprained middle finger on his throwing hand – an injury suffered late in Sunday’s win over the Bills – Smith says the injury isn’t a problem and he’ll play against the Giants.

Smith says he’s eager to play the Giants, the team that beat the 49ers in overtime last January to go to the Super Bowl.

“There’s a lot of baggage, a lot of history there,” Smith told reporters. “A little unfinished business, I guess.”